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- PDB-5g0z: Structure of native granulovirus polyhedrin determined using an X... -

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Basic information

Entry
Database: PDB / ID: 5g0z
TitleStructure of native granulovirus polyhedrin determined using an X-ray free-electron laser
ComponentsGRANULIN
KeywordsSTRUCTURAL PROTEIN / FEL / NATIVE CRYSTALS / NANO CRYSTALLOGRAPHY / SERIAL CRYSTALLOGRAPHY
Function / homologyPolyhedrin / Polyhedrin / viral occlusion body / structural molecule activity / Granulin
Function and homology information
Biological speciesCYDIA POMONELLA GRANULOVIRUS
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsGati, C. / Bunker, R.D. / Oberthur, D. / Metcalf, P. / Henry, C.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser.
Authors: Gati, C. / Oberthuer, D. / Yefanov, O. / Bunker, R.D. / Stellato, F. / Chiu, E. / Yeh, S.M. / Aquila, A. / Basu, S. / Bean, R. / Beyerlein, K.R. / Botha, S. / Boutet, S. / DePonte, D.P. / ...Authors: Gati, C. / Oberthuer, D. / Yefanov, O. / Bunker, R.D. / Stellato, F. / Chiu, E. / Yeh, S.M. / Aquila, A. / Basu, S. / Bean, R. / Beyerlein, K.R. / Botha, S. / Boutet, S. / DePonte, D.P. / Doak, R.B. / Fromme, R. / Galli, L. / Grotjohann, I. / James, D.R. / Kupitz, C. / Lomb, L. / Messerschmidt, M. / Nass, K. / Rendek, K. / Shoeman, R.L. / Wang, D. / Weierstall, U. / White, T.A. / Williams, G.J. / Zatsepin, N.A. / Fromme, P. / Spence, J.C. / Goldie, K.N. / Jehle, J.A. / Metcalf, P. / Barty, A. / Chapman, H.N.
History
DepositionMar 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.type
Revision 2.0Nov 14, 2018Group: Atomic model / Data collection / Category: atom_site / diffrn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _diffrn.pdbx_serial_crystal_experiment
Revision 2.1Aug 28, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_CC_half / _reflns.pdbx_Rmerge_I_obs ..._reflns.pdbx_CC_half / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_CC_half
Revision 2.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GRANULIN


Theoretical massNumber of molelcules
Total (without water)29,3791
Polymers29,3791
Non-polymers00
Water1,74797
1
A: GRANULIN
x 12


Theoretical massNumber of molelcules
Total (without water)352,54312
Polymers352,54312
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation8_555-z,x,-y1
Buried area75110 Å2
ΔGint-369.7 kcal/mol
Surface area128450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.400, 103.400, 103.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-2093-

HOH

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Components

#1: Protein GRANULIN / MATRIX PROTEIN / GRANULOVIRUS POLYHEDRIN


Mass: 29378.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) CYDIA POMONELLA GRANULOVIRUS / References: UniProt: P87577
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 82603

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Sample preparation

CrystalDensity Matthews: 1.61 Å3/Da / Density % sol: 23 % / Description: NONE
Crystal growDetails: IN VIVO

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.56 / Wavelength: 1.56 Å
DetectorType: CORNELL-SLAC PIXEL ARRAY DETECTOR / Detector: PIXEL / Date: Feb 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.56 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 12600 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6008 % / Biso Wilson estimate: 38.34 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.59
Reflection shellResolution: 2→2.07 Å / Redundancy: 1258 % / Mean I/σ(I) obs: 0.92 / CC1/2: 0.677 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
CrystFELV. 0.5.2data reduction
CrystFELV. 0.5.2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JVB

3jvb


Resolution: 2.001→36.557 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 20.57 / Stereochemistry target values: ML / Details: RESIDUES 1-5 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.1897 1231 9.8 %
Rwork0.1478 --
obs0.1517 12596 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.91 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.001→36.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 0 97 2120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062090
X-RAY DIFFRACTIONf_angle_d0.7392841
X-RAY DIFFRACTIONf_dihedral_angle_d19.52780
X-RAY DIFFRACTIONf_chiral_restr0.069299
X-RAY DIFFRACTIONf_plane_restr0.004371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0011-2.08120.42281280.36641275X-RAY DIFFRACTION100
2.0812-2.17590.2791500.2621215X-RAY DIFFRACTION100
2.1759-2.29060.27441210.23091277X-RAY DIFFRACTION100
2.2906-2.43410.22411390.18021237X-RAY DIFFRACTION100
2.4341-2.6220.23991290.17771256X-RAY DIFFRACTION100
2.622-2.88570.22521400.15981270X-RAY DIFFRACTION100
2.8857-3.30310.18011400.13911247X-RAY DIFFRACTION100
3.3031-4.16060.13731480.10791257X-RAY DIFFRACTION100
4.1606-36.56350.15441360.1151328X-RAY DIFFRACTION100

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